Application of Unmanned Aerial Vehicle Imagery to Quantify Benthic Primary Producer Assemblages in the Klamath River, California

Imagery from unmanned aerial vehicles (UAVs) has proven useful for mapping emerged or floating aquatic vegetation and algae, as well as submerged primary producers in shallow lakes and streams. While deeper and more turbid bodies of water with submerged primary producers are often examined by wadable observation or autonomous underwater vehicles, these methods pose challenges when water access is difficult or unsafe, or time and money are limited. Despite the growth in the use of UAVs for freshwater monitoring, there is little research on the effectiveness of UAV-based benthic algae and macrophyte detection in large, deep rivers. We provide a novel application of UAV imagery for monitoring a non-wadeable river. The Klamath River, from Iron Gate Dam in northern California to the Pacific Ocean, is ideal for investigating the presence and spatial heterogeneity of primary producer assemblages using UAV imagery because it has elevated rates of productivity, and its high velocity and depth make in situ observations difficult. We analyzed the influence of river depth, turbidity, UAV altitude, and camera angle on the effectiveness of benthic primary producer detection, and tested object and pixel-based classification methods, principal component analysis, and band ratio analysis as detection mechanisms. We quantified percent cover of algae and aquatic plants along 10 reaches of the Klamath River in June and July 2019. Aerial imagery was captured at various altitudes using a red-green-blue (RGB) camera mounted on a Phantom 4 Pro UAV, and in situ surveys conducted via swimming and snorkeling were incorporated to validate these data. Using the UAV imagery, we could detect benthic macrophytes and macroalgae at depths of up to 2m in a fairly clear river (secchi depth > 6.5 ft). Macrophytes dominated the upstream sites in closer proximity to Iron Gate Dam, while filamentous algae dominated the downstream sites below the Scott and Salmon River tributaries. In upcoming years, four proposed dam removals are expected to alter the species composition and abundance of benthic algae and macrophytes, and aerial imagery provides an effective method to monitor these changes.